The bad behavior appears not to exist in latest master as of Feb 24, 2012, nor does it exist in release 1.3.0. The code in the neighborhood of this one-line patch is significantly different than it was when the patch was made, so perhaps this issue was corrected as a side effect of some commit before the 1.3.0 release.
Mac OS X 10.6.8, 1.6.0_29, Clojure 1.3.0 test transcript:
user=> (deftype Foo [bar-quux])
user=> (def x (Foo. 1))
user=> (deftype Bar [bar-id])
user=> (Bar. 1)
user=> (deftype Baz [bar_id])
user=> (Baz. 1)